[med-svn] r4680 - in trunk/packages/mummer/trunk/debian: . patches sh-replacement-scripts
Andreas Tille
tille at alioth.debian.org
Wed Mar 24 21:34:53 UTC 2010
Author: tille
Date: 2010-03-24 21:34:48 +0000 (Wed, 24 Mar 2010)
New Revision: 4680
Added:
trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems
trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1
trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3
Removed:
trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh
trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh
trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh
Modified:
trunk/packages/mummer/trunk/debian/changelog
trunk/packages/mummer/trunk/debian/control
trunk/packages/mummer/trunk/debian/mummer.install
trunk/packages/mummer/trunk/debian/patches/10_install_dirs.patch
trunk/packages/mummer/trunk/debian/rules
Log:
Fix path problems in several scripts
Modified: trunk/packages/mummer/trunk/debian/changelog
===================================================================
--- trunk/packages/mummer/trunk/debian/changelog 2010-03-24 13:47:00 UTC (rev 4679)
+++ trunk/packages/mummer/trunk/debian/changelog 2010-03-24 21:34:48 UTC (rev 4680)
@@ -1,3 +1,22 @@
+mummer (3.22~dfsg-2) unstable; urgency=low
+
+ [ Andreas Tille ]
+ * Make sure scripts will use the installation path instead of
+ the temporary build path
+ Closes: #575105
+ * Make real use of debian/sh-replacement-scripts and drop csh
+ (build-)dependency
+ * incremented Standards-Version to reflect concordance with Debian Policy
+ 3.8.4 (no changes needed).
+ * install tandem-repeat.awk which was lacking from installation
+ previousely
+
+ [ Charles Plessy ]
+ * Updated upstream-metadata.yaml to use simple key=value form
+ instead of BibTeX entry
+
+ -- Andreas Tille <tille at debian.org> Wed, 24 Mar 2010 17:10:43 +0000
+
mummer (3.22~dfsg-1) unstable; urgency=low
* New upstream release:
Modified: trunk/packages/mummer/trunk/debian/control
===================================================================
--- trunk/packages/mummer/trunk/debian/control 2010-03-24 13:47:00 UTC (rev 4679)
+++ trunk/packages/mummer/trunk/debian/control 2010-03-24 21:34:48 UTC (rev 4680)
@@ -4,15 +4,15 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>, Andreas Tille <tille at debian.org>, Charles Plessy <plessy at debian.org>
-Build-Depends: csh, quilt, debhelper (>= 7.0.50), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended
-Standards-Version: 3.8.3
+Build-Depends: quilt, debhelper (>= 7.0.50), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended
+Standards-Version: 3.8.4
Homepage: http://mummer.sourceforge.net/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mummer/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mummer/trunk/
Package: mummer
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, perl, gawk, csh
+Depends: ${shlibs:Depends}, ${misc:Depends}, perl, gawk
Description: Efficient sequence alignment of full genomes
MUMmer is a system for rapidly aligning entire genomes, whether
in complete or draft form. For example, MUMmer 3.0 can find all
Modified: trunk/packages/mummer/trunk/debian/mummer.install
===================================================================
--- trunk/packages/mummer/trunk/debian/mummer.install 2010-03-24 13:47:00 UTC (rev 4679)
+++ trunk/packages/mummer/trunk/debian/mummer.install 2010-03-24 21:34:48 UTC (rev 4680)
@@ -1,3 +1,5 @@
debian/tmp/usr/bin/* usr/bin
debian/tmp/usr/lib/mummer/* usr/lib/mummer
scripts/Foundation.pm usr/share/perl5
+scripts/tandem-repeat.awk usr/lib/mummer
+
Modified: trunk/packages/mummer/trunk/debian/patches/10_install_dirs.patch
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/10_install_dirs.patch 2010-03-24 13:47:00 UTC (rev 4679)
+++ trunk/packages/mummer/trunk/debian/patches/10_install_dirs.patch 2010-03-24 21:34:48 UTC (rev 4680)
@@ -1,5 +1,5 @@
---- mummer-3.22~dfsg.orig/scripts/Makefile
-+++ mummer-3.22~dfsg/scripts/Makefile
+--- MUMmer3.22.orig/scripts/Makefile
++++ MUMmer3.22/scripts/Makefile
@@ -4,14 +4,19 @@
ifndef BIN_DIR
BIN_DIR := $(CURDIR)
@@ -21,55 +21,80 @@
SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))
PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
-@@ -37,7 +42,7 @@
+@@ -35,59 +40,52 @@
+
+
#-- not so PHONY rules --#
- exact-tandems: exact-tandems.csh
- $(SED) -e 's?__CSH_PATH?$(CSH)?g' \
+-exact-tandems: exact-tandems.csh
+- $(SED) -e 's?__CSH_PATH?$(CSH)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
-+ -e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \
- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
- exact-tandems.csh > $(BIN_DIR)/exact-tandems
+- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+- exact-tandems.csh > $(BIN_DIR)/exact-tandems
++exact-tandems: ../debian/sh-replacement-scripts/exact-tandems
++ cp -a $^ $(BIN_DIR)
chmod 755 $(BIN_DIR)/exact-tandems
-@@ -51,21 +56,21 @@
+
+ mapview: mapview.pl
+ $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
+- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
++ -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
+ mapview.pl > $(BIN_DIR)/mapview
+ chmod 755 $(BIN_DIR)/mapview
+
mummerplot: mummerplot.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++ -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
+ -e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \
mummerplot.pl > $(BIN_DIR)/mummerplot
chmod 755 $(BIN_DIR)/mummerplot
dnadiff: dnadiff.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++ -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
+ -e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \
dnadiff.pl > $(BIN_DIR)/dnadiff
chmod 755 $(BIN_DIR)/dnadiff
nucmer: nucmer.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
- -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
+- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++ -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
+ -e 's?__AUX_BIN_DIR?$(FINAL_AUX_BIN_DIR)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++ -e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \
nucmer.pl > $(BIN_DIR)/nucmer
chmod 755 $(BIN_DIR)/nucmer
-@@ -73,14 +78,14 @@
+
promer: promer.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
- -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
++ -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \
+ -e 's?__AUX_BIN_DIR?$(FINAL_AUX_BIN_DIR)?g' \
+ -e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \
promer.pl > $(BIN_DIR)/promer
chmod 755 $(BIN_DIR)/promer
- run-mummer1: run-mummer1.csh
- $(SED) -e 's?__CSH_PATH?$(CSH)?g' \
+-run-mummer1: run-mummer1.csh
+- $(SED) -e 's?__CSH_PATH?$(CSH)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
-+ -e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \
- run-mummer1.csh > $(BIN_DIR)/run-mummer1
+- run-mummer1.csh > $(BIN_DIR)/run-mummer1
++run-mummer1: ../debian/sh-replacement-scripts/run-mummer1
++ cp -a $^ $(BIN_DIR)
chmod 755 $(BIN_DIR)/run-mummer1
+-run-mummer3: run-mummer3.csh
+- $(SED) -e 's?__CSH_PATH?$(CSH)?g' \
+- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+- run-mummer3.csh > $(BIN_DIR)/run-mummer3
++run-mummer3: ../debian/sh-replacement-scripts/run-mummer3
++ cp -a $^ $(BIN_DIR)
+ chmod 755 $(BIN_DIR)/run-mummer3
+
+ nucmer2xfig: nucmer2xfig.pl
Modified: trunk/packages/mummer/trunk/debian/rules
===================================================================
--- trunk/packages/mummer/trunk/debian/rules 2010-03-24 13:47:00 UTC (rev 4679)
+++ trunk/packages/mummer/trunk/debian/rules 2010-03-24 21:34:48 UTC (rev 4680)
@@ -41,6 +41,9 @@
TMPDIR = $(CURDIR)/debian/tmp
BIN_DIR = $(TMPDIR)/usr/bin
AUX_BIN_DIR = $(TMPDIR)/usr/lib/mummer
+FINAL_BIN_DIR = /usr/bin
+FINAL_AUX_BIN_DIR = /usr/lib/mummer
+FINAL_SCRIPT_DIR = /usr/share/perl5/
build: $(QUILT_STAMPFN) build-stamp
build-stamp:
@@ -55,7 +58,10 @@
dh_installdirs
[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
[ -d $(AUX_BIN_DIR) ] || mkdir -p $(AUX_BIN_DIR)
- $(MAKE) BIN_DIR=$(BIN_DIR) AUX_BIN_DIR=$(AUX_BIN_DIR) CFLAGS="$(CFLAGS)"
+ $(MAKE) BIN_DIR=$(BIN_DIR) AUX_BIN_DIR=$(AUX_BIN_DIR) \
+ FINAL_BIN_DIR=$(FINAL_BIN_DIR) FINAL_AUX_BIN_DIR=$(FINAL_AUX_BIN_DIR) \
+ FINAL_SCRIPT_DIR=$(FINAL_SCRIPT_DIR) \
+ CFLAGS="$(CFLAGS)"
$(MAKE) -C docs
$(MAKE) check
# /usr/bin/annotate renamed /usr/bin/mummer-annotate for namespace and license (Artistic) reasons.
Added: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems
===================================================================
--- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems (rev 0)
+++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems 2010-03-24 21:34:48 UTC (rev 4680)
@@ -0,0 +1,35 @@
+#!/bin/sh -e
+#
+# Find exact tandem repeats in specified file involving an
+# exact duplicate of at least the specified length
+
+usage () {
+ echo "Usage: `basename $0` <file> <min-match-len>"
+ return 67 # EX_USAGE
+}
+
+if [ $# -ne 2 ] ; then
+ echo "You provided $# arguments instead of 2."
+ usage
+fi
+
+filename="$1"
+matchlen="$2"
+
+bindir=/usr/bin
+scriptdir=/usr/lib/mummer
+
+if [ ! -e "$filename" ] ; then
+ echo "File $filename does not exist."
+ usage
+fi
+
+echo "Finding matches"
+$bindir/repeat-match -t -n $matchlen "$filename" | tail +3 > $$.tmp.matches
+# This is default behavior when shell started with -e
+# if ($status != 0) exit -1
+
+echo "Tandem repeats"
+sort -k1n -k2n $$.tmp.matches | awk -f $
+$scriptdir/tandem-repeat.awk
+rm -f $$.tmp.matches
Deleted: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh
===================================================================
--- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh 2010-03-24 13:47:00 UTC (rev 4679)
+++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh 2010-03-24 21:34:48 UTC (rev 4680)
@@ -1,34 +0,0 @@
-#!/bin/sh -e
-#
-# Find exact tandem repeats in specified file involving an
-# exact duplicate of at least the specified length
-
-usage () {
- echo "Usage: `basename $0` <file> <min-match-len>"
- return 67 # EX_USAGE
-}
-
-if [ $# -ne 2 ] ; then
- echo "You provided $# arguments instead of 2."
- usage
-fi
-
-filename="$1"
-matchlen="$2"
-
-bindir=__BIN_DIR
-scriptdir=__SCRIPT_DIR
-
-if [ ! -e "$filename" ] ; then
- echo "File $filename does not exist."
- usage
-fi
-
-echo "Finding matches"
-$bindir/repeat-match -t -n $matchlen "$filename" | tail +3 > $$.tmp.matches
-# This is default behavior when shell started with -e
-# if ($status != 0) exit -1
-
-echo "Tandem repeats"
-sort -k1n -k2n $$.tmp.matches | awk -f $scriptdir/tandem-repeat.awk
-rm -f $$.tmp.matches
Added: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1
===================================================================
--- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1 (rev 0)
+++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1 2010-03-24 21:34:48 UTC (rev 4680)
@@ -0,0 +1,45 @@
+#!/bin/sh -e
+#
+# **SEVERELY** antiquated script for running the mummer 1 suite
+# -r option reverse complements the query sequence, coordinates of the reverse
+# matches will be relative to the reversed sequence
+#
+
+usage () {
+ echo "Usage: `basename $0` <fasta reference> <fasta query> <prefix> [-r]"
+ return 67 # EX_USAGE
+}
+
+if [ $# -ne 3 -a $# -ne 4 ] ; then
+ echo "You provided $# arguments."
+ usage
+fi
+
+ref="$1"
+qry="$2"
+pfx="$3"
+rev="$4"
+
+bindir=/usr/bin
+
+if [ ! -e "$ref" ] ; then
+ echo "File for fasta reference $ref does not exist."
+ usage
+fi
+
+if [ ! -e "$qry" ] ; then
+ echo "File for fasta query $qry does not exist."
+ usage
+fi
+
+if [ "$pfx" = "" ] ; then
+ usage
+fi
+
+echo "Find MUMs"
+$bindir/mummer -mum -l 20 "$rev" "$ref" "$qry" | tail +2 > "$pfx".out
+echo "Determine gaps"
+$bindir/gaps "$ref" "$rev" < "$pfx".out > "$pfx".gaps
+echo "Align gaps"
+$bindir/mummer-annotate "$pfx".gaps "$qry" > "$pfx".align
+mv witherrors.gaps "$pfx".errorsgaps
Deleted: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh
===================================================================
--- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh 2010-03-24 13:47:00 UTC (rev 4679)
+++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh 2010-03-24 21:34:48 UTC (rev 4680)
@@ -1,45 +0,0 @@
-#!/bin/sh -e
-#
-# **SEVERELY** antiquated script for running the mummer 1 suite
-# -r option reverse complements the query sequence, coordinates of the reverse
-# matches will be relative to the reversed sequence
-#
-
-usage () {
- echo "Usage: `basename $0` <fasta reference> <fasta query> <prefix> [-r]"
- return 67 # EX_USAGE
-}
-
-if [ $# -ne 3 -a $# -ne 4 ] ; then
- echo "You provided $# arguments."
- usage
-fi
-
-ref="$1"
-qry="$2"
-pfx="$3"
-rev="$4"
-
-bindir=__BIN_DIR
-
-if [ ! -e "$ref" ] ; then
- echo "File for fasta reference $ref does not exist."
- usage
-fi
-
-if [ ! -e "$qry" ] ; then
- echo "File for fasta query $qry does not exist."
- usage
-fi
-
-if [ "$pfx" = "" ] ; then
- usage
-fi
-
-echo "Find MUMs"
-$bindir/mummer -mum -l 20 "$rev" "$ref" "$qry" | tail +2 > "$pfx".out
-echo "Determine gaps"
-$bindir/gaps "$ref" "$rev" < "$pfx".out > "$pfx".gaps
-echo "Align gaps"
-$bindir/mummer-annotate "$pfx".gaps "$qry" > "$pfx".align
-mv witherrors.gaps "$pfx".errorsgaps
Added: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3
===================================================================
--- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3 (rev 0)
+++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3 2010-03-24 21:34:48 UTC (rev 4680)
@@ -0,0 +1,47 @@
+#!/bin/sh -e
+#
+# for running the basic mummer 3 suite, should use nucmer instead when possible
+# to avoid the confusing reverse coordinate system of the raw programs.
+#
+# NOTE: be warned that all reverse matches will then
+# be relative to the reverse complement of the query sequence.
+#
+# Edit this script as necessary to alter the matching and clustering values
+#
+
+usage () {
+ echo "Usage: `basename $0` <fasta reference> <multi-fasta query> <prefix>"
+ return 67 # EX_USAGE
+}
+
+if [ $# -ne 3 ] ; then
+ echo "You provided $# arguments."
+ usage
+fi
+
+ref="$1"
+qry="$2"
+pfx="$3"
+
+bindir=/usr/bin
+
+if [ ! -e "$ref" ] ; then
+ echo "File for fasta reference $ref does not exist."
+ usage
+fi
+
+if [ ! -e "$qry" ] ; then
+ echo "File for fasta query $qry does not exist."
+ usage
+fi
+
+if [ "$pfx" = "" ] ; then
+ usage
+fi
+
+echo "Find MUMs"
+$bindir/mummer -mumreference -b -l 20 "$ref" "$qry" > "$pfx".out
+echo "Determine gaps"
+$bindir/mgaps -l 100 -f .12 -s 600 < "$pfx".out > "$pfx".gaps
+echo "Align gaps"
+$bindir/combineMUMs -x -e .10 -W "$pfx".errorsgaps "$ref" "$qry" "$pfx".gaps > "$pfx".align
Deleted: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh
===================================================================
--- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh 2010-03-24 13:47:00 UTC (rev 4679)
+++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh 2010-03-24 21:34:48 UTC (rev 4680)
@@ -1,47 +0,0 @@
-#!/bin/sh -e
-#
-# for running the basic mummer 3 suite, should use nucmer instead when possible
-# to avoid the confusing reverse coordinate system of the raw programs.
-#
-# NOTE: be warned that all reverse matches will then
-# be relative to the reverse complement of the query sequence.
-#
-# Edit this script as necessary to alter the matching and clustering values
-#
-
-usage () {
- echo "Usage: `basename $0` <fasta reference> <multi-fasta query> <prefix>"
- return 67 # EX_USAGE
-}
-
-if [ $# -ne 3 ] ; then
- echo "You provided $# arguments."
- usage
-fi
-
-ref="$1"
-qry="$2"
-pfx="$3"
-
-bindir=__BIN_DIR
-
-if [ ! -e "$ref" ] ; then
- echo "File for fasta reference $ref does not exist."
- usage
-fi
-
-if [ ! -e "$qry" ] ; then
- echo "File for fasta query $qry does not exist."
- usage
-fi
-
-if [ "$pfx" = "" ] ; then
- usage
-fi
-
-echo "Find MUMs"
-$bindir/mummer -mumreference -b -l 20 "$ref" "$qry" > "$pfx".out
-echo "Determine gaps"
-$bindir/mgaps -l 100 -f .12 -s 600 < "$pfx".out > "$pfx".gaps
-echo "Align gaps"
-$bindir/combineMUMs -x -e .10 -W "$pfx".errorsgaps "$ref" "$qry" "$pfx".gaps > "$pfx".align
More information about the debian-med-commit
mailing list